Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate HSERO_RS19435 HSERO_RS19435 anthranilate synthase subunit I
Query= BRENDA::P9WFX1 (450 letters) >FitnessBrowser__HerbieS:HSERO_RS19435 Length = 498 Score = 127 bits (318), Expect = 1e-33 Identities = 99/304 (32%), Positives = 147/304 (48%), Gaps = 28/304 (9%) Query: 149 RLFDAGIRHREAIDRLLATG------VREVPQSRSVDVSDDPSGFRRRVAVAVDEIAAGR 202 RL D R D + TG +RE P+ + + VA A + + AG Sbjct: 190 RLRDLRAMLRRPADAPVTTGSVRTETIREFPKDE----------YLKAVARAKEYVMAGD 239 Query: 203 YHKVILSRCVEVPFAIDFPLT-YRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADG 261 +V + + ++ + +D PL YR R N + G ++ +G SPE++ + G Sbjct: 240 LMQVQIGQRLKKSY-VDSPLMLYRALRSLNPSPYMYFYNFGDMQIVGASPEILVRNESIG 298 Query: 262 V----VITEPLAGTRALGRGPAIDR---LARDDLESNSKEIVEHAISVRSSLEEITDIAE 314 + PLAGTR RG I+R LAR+ L ++ KEI EH + + + +I IA Sbjct: 299 EGQKKITIRPLAGTRP--RGSTIERDEQLARE-LLADPKEIAEHVMLIDLARNDIGRIAT 355 Query: 315 PGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAI 374 GS V D M + + VQH+ S + L P + L+A FPA T SG PK +E I Sbjct: 356 TGSVKVTDQMVIEKYSHVQHIVSNVEGILKPGMSNLDVLKATFPAGTLSGAPKVRAMEII 415 Query: 375 FRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEE 434 L+ RG+Y GA LS G +D A+ +R G +++A AGI+ +S PE E+EE Sbjct: 416 DELEPTKRGIYGGACGYLSFGGEMDVAIAIRTGVIKDGTLYVQAAAGIVADSVPEMEWEE 475 Query: 435 TCEK 438 T K Sbjct: 476 TENK 479 Lambda K H 0.319 0.135 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 433 Number of extensions: 22 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 450 Length of database: 498 Length adjustment: 33 Effective length of query: 417 Effective length of database: 465 Effective search space: 193905 Effective search space used: 193905 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory